Zübeyir Devran

Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing

Abstract It is imperative to identify highly polymorphic and tightly linked markers of a known trait for molecular marker-assisted selection. Potyvirus resistance 4 (Pvr4) locus in pepper confers resistance to three pathotypes of potato virus Y and to pepper mottle virus. We describe the use of next-generation sequencing technology to generate molecular markers tightly linked to Pvr4. Initially, comparative genomics was carried out, and a syntenic region of tomato on chromosome ten was used to generate PCR-based markers and map Pvr4. Subsequently, the genomic sequence of pepper was used, and more than 5000 single-nucleotide variants (SNVs) were identified within the interval. In addition, we identified nucleotide binding site–leucine-rich repeat-type disease resistance genes within the interval. Several of these SNVs were converted to molecular markers desirable for large-scale molecular breeding programmes.

AFLP and SRAP markers linked to the mj gene for root-knot nematode resistance in cucumber

Nematoides causadores de galhas (Meloidogyne spp.) em raizes de pepino Cucumis sativus L.) sao de ocorrencia mundial. Marcadores moleculares ligados ao gene mj que confere resistencia a M. javanica em pepino podem auxiliar na selecao de plantas em programas de melhoramento genetico. Cem AFLP (EcoRI-MseI) e 112 SRAP foram usados para a selecao de parentais resistentes e susceptiveis, por meio de polimorfismos, para o desenvolvimento de marcadores moleculares ligados ao gene mj. Entre 100 oligonucleotideos iniciadores para AFLP, 92 geraram fragmentos amplificados de DNA e dois produziram candidatos a marcadores (E-ATT/M-CAA e E-AAC/M-CTG). Os dois fragmentos amplificados foram clonados e sequenciados. Oligonucleotideos iniciadores sintetizados a partir das sequencias de nucleotideos obtidas nao produziram fragmentos polimorficos entre os parentais. Alem disso, as sequencias de nucleotideos nao contem sitios de restricoes ou delecoes que possam ser convertidos em marcadores CAPS ou SCAR. As duas sequencias de nucleotideos obtidas para os marcadores polimorficos AFLP foram usadas primeiramente para sintetizar os oligonucleotideos iniciadores especificos D1F, D1R, D17F e D17R. Oligonucleotideos iniciadores senso e antisenso para SRAP foram usados em combinacoes com os quatro oligonucleotideos iniciadores especificos para identificacao de polimorfismos entre os parentais. Dentre 112 combinacoes testadas, 11 geraram polimorfismos entre individuos parentais. O programa MapMaker Exp 3.0 foi usado para analise desses 11 marcadores. Foram identificados dois marcadores inseridos no gene mj nas distancias de 16.3 e 19.3 cM. Os resultados indicam que esses marcadores podem ser usados para o desenvolvimento de marcadores moleculares para o gene mj.

Genetic characterization of Meloidogyne incognita isolates from Turkey using sequence-related amplified polymorphism (SRAP)

Southern root knot nematode Meloidogyne incognita is the most widespread-species, causing serious yield losses in protected vegetables fields in the West Mediterranean region of Turkey. The knowledge of genetic variation within M. incognita is required for disease management and improvement of resistant varieties by breeding programs. In the present study, the isolates were classified into different groups based on sequence-related amplified polymorphism (SRAP) fingerprints. To our knowledge, this is the first study carried out on the characterization of M. incognita isolates using SRAP. The schematic diagram by tested primers to differentiate of M. incognita isolates was formed in discrimination of nematodes as an effective molecular tool since it is cost effective and easiness. Data presents a genetic variation on root-knot nematode species. These selected SRAP markers can be used to follow genetic structure and differentiation on M. incognita isolates in a certain region.

A rapid molecular detection method for Aphelenchoides besseyi from rice tissues

Rice is an important agricultural crop providing nutrition for humans worldwide. Rice white tip nematode, Aphelenchoides besseyi, is a nematode causing economic yield losses globally in rice-growing areas. Because A. besseyi is a seed-transmitted nematode, its rapid and accurate identification is important for seed certification and quarantine purposes. Here, we developed species-specific primers for the small subunit ribosomal DNA region of the Aphelenchoides genus to identify A. besseyi. DNA was extracted from juveniles and directly infected tissues, such as hulls, brown rice and paddy rice. A. besseyi was easily and rapidly detected from plant tissues without nematode extraction. Because the extraction of A. besseyi from plant tissues is time-consuming and labour-intensive, the developed method may be applied to seed certification and quarantine approaches. To our knowledge, this is the first report directly identifying A. besseyi from infected plant tissues.

Response of heat-stable tomato genotypes to Mi-1 virulent root-knot nematode populations

Summary Tomato is one of the most important vegetables cultivated worldwide. Many pests and pathogens cause significant yield decline in growing fields. Root-knot nematodes are known to be devastating pathogens on tomato. Resistant varieties carrying Mi-1 gene have been effectively used to control of root-knot nematodes. However, the efficiency of Mi-1 has been especially restricted by virulent root-knot nematode populations in cultivated tomatoes. Therefore, new resistant genetic varieties are required in growing fields. Heat-stable wild tomato species are known to be resistance to Meloidogyne populations at high soil temperature. To our knowledge, there are limited studies on response of heat-stable materials to different virulent root knot nematode populations under 28 o C. In the present study, reactions of heat stable materials to different virulent isolates of M. incognita and M. javanica were investigated at 24 o C soil temperature. Results showed that these materials did not confer resistance against M. incognita and M. javanica virulent isolates. Therefore, searching of new genetic sources resistant to virulent root-knot nematodes is required for breeding program.

Bitki paraziti nematodların beslenme stratejileri

Bitki paraziti nematodlar, dunya genelinde tarim urunlerinin en onemli zararlilarindan birisidir. Gunumuze kadar bitkilerde zararlara neden olan yaklasik olarak 4100 tur tanimlanmistir. Bitki paraziti nematodlar kok, sap, yaprak ve tohum gibi tum bitki kisimlarinda beslenebilmektedirler. Nematodlar canli bitki dokularinda beslenmektedir ve konukculariyla cok farkli etkilesimler icerisine girmektedirler. Bitkilerde genel olarak ektoparazitik, yari endoparazitik, endoparazitik ve gezici ekto-endoparazitik seklinde beslenmektedirler. Ektoparazitler konukcuya giris yapmazken yari endoparazitik nematodlar vucutlarinin belli bir kismini doku icerisine olacak sekilde beslenmelerine devam etmektedirler. Endoparazitik nematodlar tamamen kok icerisinde beslenmektedirler. Gezici ekto-endo parazitik nematodlar ipliksi yapida ve yalnizca bas bolgelerini bitki dokularina sokmakta ve kortikal hucrelerden beslenmektedirler. Ayrica bu beslenme tiplerinin alt gruplarida bulunmaktadir. Bitki paraziti nematodlarin beslenme tipleriyle ilgili bilgi, bu zararlilarla mucadele stratejilerinin belirlenmesi icin onemlidir. Bu derlemede bitki paraziti nematodlarin beslenme stratejilerini tanitmak icin hazirlanmistir.

A novel multiplex PCR tool for simultaneous detection of three root-knot nematodes

Root-knot nematodes, Meloidogyne incognita, M. javanica and M. arenaria, cause serious yield losses in protected growing areas in Turkey. They also show a‘co-infection’ profile in fields’ soil microflora. In this study, we designed multiplex primers for detecting all three species simultaneously. Additionally, the confidence and definition of this method were tested by using mixed and large populations related to these species at different biological stages. We suggest this effective tool be used to easily identify three root-knot nematodes that will be beneficial for designing crop rotation modelling in protected growing areas in Turkey as well as quarantine requirements.

Batı Akdeniz Bölgesi örtüaltı yetiştiriciliğinde sorun olan domateste Bakteriyel Benek (Pseudomonas syringae pv. tomato “Okabe” Y.D.&W) hastalık etmeni izolatlarının genetik farklılıklarının moleküler yöntemlerle tespiti

Bu calismanin amaci, Bati Akdeniz Bolgesi ortualti domates yetistiriciliginde onemli olan Bakteriyel Benek ( Pst ) hastalik etmeninin klasik ve molekuler yontemlerle tanilanmasi ve Pst izolatlarinin genetik farkliliklarinin ISSR ve SRAP markirlari kullanilarak molekuler yontemlerle belirlenmesidir. Calisma kapsaminda, Bati Akdeniz Bolgesi’nde domates yetistiriciliginde ortaya cikan hastalik etmeninin ( Pst izolatlarinin ) toplanmasi icin survey calismalari yapilmistir. Survey calismasi suresince gudumlu ornekleme yapilmis ve 10 tane Pst izolati toplanmistir. Patojen izole edildikten sonra biyokimyasal ve molekuler yontemlerle tanilanmistir. Pst izolatlari arasindaki genetiksel farkliliklar ISSR (Inter Simple Sequence Repeat) ve SRAP (Sequence-Related Amplified Polymorphism) molekuler markirlar ile belirlenmeye calisilmistir. Sonuc olarak, patojenin bolgede iklim sartlarina bagli olarak goruldugu ve klasik ve molekuler olarak basariyla tespit edilebildigi sonucuna varilmistir.

Kök-ur Nematodları ve Konukçuları Arasındaki İlişkiler

Kok ur nematodlari (Meloidogyne spp.), bircok bitki turunun zorunlu ve biyotrofik patojenidir. Bunlar endoparazit olup, konukcularinin kokleri icerisinde yasarlar. Meloidogyne turleri, Turkiye’de ozellikle ortu alti uretim alanlarinda ekonomik kayiplara neden olmaktadir. Kok-ur nematodlari, hassas konukcu bitkilerinin koklerinde tipik urlanmalara neden olurlar. Bu nedenle, kokler tarafindan su ve besin alimi azalmakta buda bitkilerde gelismede durgunluk, solgunluk, verimde azalma ve toprak kokenli patojenlere hassasiyet olusturmaktadir. Bu calismada; kok-ur nematodlarinin tanimlanmasi, yayilisi, yasam dongusu, belirtileri ve konukculariyla olan iliskileri hakkinda bilgi verilmistir

Kök lezyon nematodları (Pratylenchus spp.)'nın sert ve yumuşak çekirdekli meyve anaçlarında konukçu reaksiyonları

Pratylenchus thornei, P. neglectus, P. penetrans and P. crenatus are common distributed Root lesion nematodes of temperate fruit orchards in the West Mediterranean region of Turkey. The objective of this study was to investigate host reaction of these root lesion nematodes on commonly used apple, cherry, peach and pear rootstocks in Turkey. Experiments were established on randomized block desing in screen house with 5 replica. Pratylenchus penetrans developed well and had high population density on the M-9, MM-106 and MM-111 apple rootstocks in year 1. Reproduction factor (Rf) of P. penetrans on M-9, MM-106 and MM-111 in the first year were 6,2, 3,0 and 12,9, respectively. In the second year, Rf of P. penetrans on M-9, MM-106 and MM-111 were 5,6, 2,5 and 10,6, respectively. OHF-333 and Quince-A pear rootstocks showed moderate resistant reaction to P. penetrans. Rf value of P. penetrans was found 1,0 on OHF 333 and 0,5 on Quince-A rootstocks in the first year. And also, similar results were observed on pear rootstocks in the second year. Peach rootstocks GF- 677 showed moderate susceptible reaction to P. penetrans in both two year. Nemaguard, GN (Garnem) and Myrabolon 29 C rootstocks had resistant to P. penetrans. Similarly, P. penetrans did not reproduce on Cherry rootstocks SL-64, Maxma-14 and Gisela-5 in years 1 and 2. Pratylenchus crenatus, P. thornei and P. neglectus did not develope and Rf value of these lesion nematodes were determined lower than 1 value on apple, cherry, peach and pear rootstocks in the experiments.